forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java

   1
   2 package org.forester.archaeopteryx;
   3
   4 import java.awt.BorderLayout;
   5 import java.awt.Container;
   6 import java.awt.event.ActionEvent;
   7 import java.awt.event.ActionListener;
   8 import java.awt.event.ComponentAdapter;
   9 import java.awt.event.ComponentEvent;
  10 import java.io.ByteArrayOutputStream;
  11 import java.io.File;
  12 import java.io.IOException;
  13 import java.net.URL;
  14 import java.util.LinkedList;
  15 import java.util.List;
  16 import java.util.NoSuchElementException;
  17
  18 import javax.swing.ButtonGroup;
  19 import javax.swing.JApplet;
  20 import javax.swing.JCheckBoxMenuItem;
  21 import javax.swing.JMenu;
  22 import javax.swing.JMenuBar;
  23 import javax.swing.JMenuItem;
  24 import javax.swing.JOptionPane;
  25 import javax.swing.JRadioButtonMenuItem;
  26 import javax.swing.UIManager;
  27 import javax.swing.UnsupportedLookAndFeelException;
  28 import javax.swing.event.ChangeEvent;
  29 import javax.swing.event.ChangeListener;
  30
  31 import org.apache.commons.codec.binary.Base64;
  32 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
  33 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  34 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
  35 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
  36 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
  37 import org.forester.phylogeny.Phylogeny;
  38 import org.forester.phylogeny.PhylogenyMethods;
  39 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
  40 import org.forester.phylogeny.data.SequenceRelation;
  41 import org.forester.sdi.GSDI;
  42 import org.forester.sdi.GSDIR;
  43 import org.forester.sdi.SDIException;
  44 import org.forester.util.ForesterConstants;
  45 import org.forester.util.ForesterUtil;
  46
  47 // Use like this:
  48 // <applet archive="forester.jar"
  49 // code="org.forester.archaeopteryx.ArchaeopteryxE.class"
  50 // codebase="http://www.myserver.org/path/to/forester"
  51 // width="600"
  52 // height="500"
  53 // alt="ArchaeopteryxE is not working on your system (requires at least Sun Java 1.5)!">
  54 // <param name="url_of_tree_to_load"
  55 // value="http://www.myserver.org/examples/data/apaf.xml">
  56 // <param name="config_file"
  57 // value="http://www.myserver.org/examples/config/config_file.txt">
  58 // </applet>
  59 public class ArchaeopteryxE extends JApplet implements ActionListener {
  60
  61     private final static String         NAME             = "ArchaeopteryxE";
  62     private static final long           serialVersionUID = -1220055577935759443L;
  63     private Configuration               _configuration;
  64     private MainPanelApplets            _mainpanel;
  65     private JMenuBar                    _jmenubar;
  66     private JMenu                       _options_jmenu;
  67     private JMenu                       _font_size_menu;
  68     private JMenuItem                   _super_tiny_fonts_mi;
  69     private JMenuItem                   _tiny_fonts_mi;
  70     private JMenuItem                   _small_fonts_mi;
  71     private JMenuItem                   _medium_fonts_mi;
  72     private JMenuItem                   _large_fonts_mi;
  73     private JMenu                       _tools_menu;
  74     private JMenuItem                   _taxcolor_item;
  75     private JMenuItem                   _confcolor_item;
  76     private JMenuItem                   _midpoint_root_item;
  77     private JMenu                       _view_jmenu;
  78     private JMenuItem                   _view_as_XML_item;
  79     private JMenuItem                   _view_as_NH_item;
  80     private JMenuItem                   _view_as_nexus_item;
  81     private JMenuItem                   _display_basic_information_item;
  82     private JMenu                       _type_menu;
  83     private JCheckBoxMenuItem           _rectangular_type_cbmi;
  84     private JCheckBoxMenuItem           _triangular_type_cbmi;
  85     private JCheckBoxMenuItem           _curved_type_cbmi;
  86     private JCheckBoxMenuItem           _convex_type_cbmi;
  87     private JCheckBoxMenuItem           _euro_type_cbmi;
  88     private JCheckBoxMenuItem           _rounded_type_cbmi;
  89     private JCheckBoxMenuItem           _unrooted_type_cbmi;
  90     private JCheckBoxMenuItem           _circular_type_cbmi;
  91     private JMenuItem                   _help_item;
  92     private JMenuItem                   _about_item;
  93     private JMenu                       _help_jmenu;
  94     private JMenuItem                   _website_item;
  95     private JMenuItem                   _phyloxml_website_item;
  96     private JMenuItem                   _phyloxml_ref_item;
  97     private JMenuItem                   _aptx_ref_item;
  98     private JMenuItem                   _remove_branch_color_item;
  99     private JMenuItem                   _remove_visual_styles_item;
 100     private JCheckBoxMenuItem           _show_domain_labels;
 101     private JCheckBoxMenuItem           _show_annotation_ref_source;
 102     private JCheckBoxMenuItem           _color_labels_same_as_parent_branch;
 103     private JCheckBoxMenuItem           _abbreviate_scientific_names;
 104     private JCheckBoxMenuItem           _screen_antialias_cbmi;
 105     private JCheckBoxMenuItem           _background_gradient_cbmi;
 106     private JCheckBoxMenuItem           _color_by_taxonomic_group_cbmi;
 107     private JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;
 108     private JRadioButtonMenuItem        _uniform_cladograms_rbmi;
 109     private JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;
 110     private Options                     _options;
 111     private JMenuItem                   _choose_font_mi;
 112     private JMenuItem                   _switch_colors_mi;
 113     JCheckBoxMenuItem                   _label_direction_cbmi;
 114     private JCheckBoxMenuItem           _show_scale_cbmi;
 115     private JCheckBoxMenuItem           _search_case_senstive_cbmi;
 116     private JCheckBoxMenuItem           _search_whole_words_only_cbmi;
 117     private JCheckBoxMenuItem           _inverse_search_result_cbmi;
 118     private JCheckBoxMenuItem           _show_overview_cbmi;
 119     private JMenuItem                   _choose_minimal_confidence_mi;
 120     private JCheckBoxMenuItem           _show_branch_length_values_cbmi;
 121     private JMenuItem                   _collapse_species_specific_subtrees;
 122     private JMenuItem                   _overview_placment_mi;
 123     private ButtonGroup                 _radio_group_1;
 124     private JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;
 125     private JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;
 126     private JMenuItem                   _cycle_node_shape_mi;
 127     private JMenuItem                   _cycle_node_fill_mi;
 128     private JMenuItem                   _choose_node_size_mi;
 129     private JCheckBoxMenuItem           _show_confidence_stddev_cbmi;
 130     private final LinkedList<TextFrame> _textframes      = new LinkedList<TextFrame>();
 131     private JMenu                       _analysis_menu;
 132     private JMenuItem                   _gsdi_item;
 133     private JMenuItem                   _gsdir_item;
 134     private Phylogeny                   _species_tree;
 135     private JCheckBoxMenuItem           _right_line_up_domains_cbmi;
 136     private JCheckBoxMenuItem           _line_up_renderable_data_cbmi;
 137
 138     @Override
 139     public void actionPerformed( final ActionEvent e ) {
 140         final Object o = e.getSource();
 141         if ( o == _midpoint_root_item ) {
 142             getMainPanel().getCurrentTreePanel().midpointRoot();
 143         }
 144         else if ( o == _gsdi_item ) {
 145             if ( isSubtreeDisplayed() ) {
 146                 return;
 147             }
 148             executeGSDI();
 149         }
 150         else if ( o == _gsdir_item ) {
 151             if ( isSubtreeDisplayed() ) {
 152                 return;
 153             }
 154             executeGSDIR();
 155         }
 156         else if ( o == _taxcolor_item ) {
 157             getMainPanel().getCurrentTreePanel().taxColor();
 158         }
 159         else if ( o == _confcolor_item ) {
 160             getMainPanel().getCurrentTreePanel().confColor();
 161         }
 162         else if ( o == _collapse_species_specific_subtrees ) {
 163             if ( getCurrentTreePanel() != null ) {
 164                 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
 165             }
 166         }
 167         else if ( o == _remove_branch_color_item ) {
 168             removeBranchColors();
 169         }
 170         else if ( o == _remove_visual_styles_item ) {
 171             removeVisualStyles();
 172         }
 173         else if ( o == _switch_colors_mi ) {
 174             switchColors();
 175         }
 176         else if ( o == _display_basic_information_item ) {
 177             displayBasicInformation();
 178         }
 179         else if ( o == _view_as_NH_item ) {
 180             viewAsNH();
 181         }
 182         else if ( o == _view_as_XML_item ) {
 183             viewAsXML();
 184         }
 185         else if ( o == _view_as_nexus_item ) {
 186             viewAsNexus();
 187         }
 188         else if ( o == _super_tiny_fonts_mi ) {
 189             if ( getCurrentTreePanel() != null ) {
 190                 getCurrentTreePanel().setSuperTinyFonts();
 191                 getCurrentTreePanel().repaint();
 192             }
 193         }
 194         else if ( o == _tiny_fonts_mi ) {
 195             if ( getCurrentTreePanel() != null ) {
 196                 getCurrentTreePanel().setTinyFonts();
 197                 getCurrentTreePanel().repaint();
 198             }
 199         }
 200         else if ( o == _small_fonts_mi ) {
 201             if ( getCurrentTreePanel() != null ) {
 202                 getCurrentTreePanel().setSmallFonts();
 203                 getCurrentTreePanel().repaint();
 204             }
 205         }
 206         else if ( o == _medium_fonts_mi ) {
 207             if ( getCurrentTreePanel() != null ) {
 208                 getCurrentTreePanel().setMediumFonts();
 209                 getCurrentTreePanel().repaint();
 210             }
 211         }
 212         else if ( o == _large_fonts_mi ) {
 213             if ( getCurrentTreePanel() != null ) {
 214                 getCurrentTreePanel().setLargeFonts();
 215                 getCurrentTreePanel().repaint();
 216             }
 217         }
 218         else if ( o == _choose_font_mi ) {
 219             chooseFont();
 220         }
 221         else if ( o == _choose_minimal_confidence_mi ) {
 222             chooseMinimalConfidence();
 223         }
 224         else if ( o == _choose_node_size_mi ) {
 225             MainFrame.chooseNodeSize( getOptions(), this );
 226         }
 227         else if ( o == _overview_placment_mi ) {
 228             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
 229         }
 230         else if ( o == _cycle_node_fill_mi ) {
 231             MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
 232         }
 233         else if ( o == _cycle_node_shape_mi ) {
 234             MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
 235         }
 236         else if ( o == _non_lined_up_cladograms_rbmi ) {
 237             updateOptions( getOptions() );
 238             _mainpanel.getControlPanel().showWhole();
 239         }
 240         else if ( o == _uniform_cladograms_rbmi ) {
 241             updateOptions( getOptions() );
 242             _mainpanel.getControlPanel().showWhole();
 243         }
 244         else if ( o == _ext_node_dependent_cladogram_rbmi ) {
 245             updateOptions( getOptions() );
 246             _mainpanel.getControlPanel().showWhole();
 247         }
 248         else if ( o == _search_case_senstive_cbmi ) {
 249             updateOptions( getOptions() );
 250             getMainPanel().getControlPanel().search0();
 251             getMainPanel().getControlPanel().search1();
 252         }
 253         else if ( o == _search_whole_words_only_cbmi ) {
 254             updateOptions( getOptions() );
 255             getMainPanel().getControlPanel().search0();
 256             getMainPanel().getControlPanel().search1();
 257         }
 258         else if ( o == _inverse_search_result_cbmi ) {
 259             updateOptions( getOptions() );
 260             getMainPanel().getControlPanel().search0();
 261             getMainPanel().getControlPanel().search1();
 262         }
 263         else if ( o == _show_scale_cbmi ) {
 264             updateOptions( getOptions() );
 265         }
 266         else if ( o == _show_branch_length_values_cbmi ) {
 267             updateOptions( getOptions() );
 268         }
 269         else if ( o == _show_confidence_stddev_cbmi ) {
 270             updateOptions( getOptions() );
 271         }
 272         else if ( o == _label_direction_cbmi ) {
 273             updateOptions( getOptions() );
 274         }
 275         else if ( o == _abbreviate_scientific_names ) {
 276             updateOptions( getOptions() );
 277         }
 278         else if ( o == _show_overview_cbmi ) {
 279             updateOptions( getOptions() );
 280             if ( getCurrentTreePanel() != null ) {
 281                 getCurrentTreePanel().updateOvSizes();
 282             }
 283         }
 284         else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
 285                 || ( o == _convex_type_cbmi ) || ( o == _rounded_type_cbmi ) || ( o == _euro_type_cbmi )
 286                 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
 287             typeChanged( o );
 288         }
 289         else if ( o == _screen_antialias_cbmi ) {
 290             updateOptions( getOptions() );
 291             setupScreenTextAntialias( getMainPanel().getTreePanels(), isScreenAntialias() );
 292         }
 293         else if ( o == _background_gradient_cbmi ) {
 294             updateOptions( getOptions() );
 295         }
 296         else if ( o == _show_domain_labels ) {
 297             updateOptions( getOptions() );
 298         }
 299         else if ( o == _color_labels_same_as_parent_branch ) {
 300             updateOptions( getOptions() );
 301         }
 302         else if ( o == _show_default_node_shapes_internal_cbmi ) {
 303             updateOptions( getOptions() );
 304         }
 305         else if ( o == _show_default_node_shapes_external_cbmi ) {
 306             updateOptions( getOptions() );
 307         }
 308         else if ( o == _about_item ) {
 309             MainFrame.about();
 310         }
 311         else if ( o == _help_item ) {
 312             try {
 313                 AptxUtil.openWebsite( Constants.APTX_DOC_SITE, true, this );
 314             }
 315             catch ( final IOException e1 ) {
 316                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 317             }
 318         }
 319         else if ( o == _website_item ) {
 320             try {
 321                 AptxUtil.openWebsite( Constants.APTX_WEB_SITE, true, this );
 322             }
 323             catch ( final IOException e1 ) {
 324                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 325             }
 326         }
 327         else if ( o == _phyloxml_website_item ) {
 328             try {
 329                 AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, true, this );
 330             }
 331             catch ( final IOException e1 ) {
 332                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 333             }
 334         }
 335         else if ( o == _aptx_ref_item ) {
 336             try {
 337                 AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, true, this );
 338             }
 339             catch ( final IOException e1 ) {
 340                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 341             }
 342         }
 343         else if ( o == _phyloxml_ref_item ) {
 344             try {
 345                 AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, true, this );
 346             }
 347             catch ( final IOException e1 ) {
 348                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
 349             }
 350         }
 351         else if ( o == _color_by_taxonomic_group_cbmi ) {
 352             updateOptions( getOptions() );
 353         }
 354         else if ( o == _line_up_renderable_data_cbmi ) {
 355             if ( !_line_up_renderable_data_cbmi.isSelected() ) {
 356                 _right_line_up_domains_cbmi.setSelected( false );
 357             }
 358             updateOptions( getOptions() );
 359         }
 360         else if ( o == _right_line_up_domains_cbmi ) {
 361             if ( _right_line_up_domains_cbmi.isSelected() ) {
 362                 _line_up_renderable_data_cbmi.setSelected( true );
 363             }
 364             updateOptions( getOptions() );
 365         }
 366         repaint();
 367     }
 368
 369     @Override
 370     public void destroy() {
 371         AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
 372         removeAllTextFrames();
 373         if ( getMainPanel() != null ) {
 374             getMainPanel().terminate();
 375         }
 376     }
 377
 378     /**
 379      * This method returns the current external node data which
 380      * has been selected by the user by clicking the "Return ..."
 381      * menu item. This method is expected to be called from Javascript or
 382      * something like it.
 383      *
 384      * @return current external node data as String
 385      */
 386     public String getCurrentExternalNodesDataBuffer() {
 387         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
 388     }
 389
 390     public int getCurrentExternalNodesDataBufferChangeCounter() {
 391         return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
 392     }
 393
 394     public int getCurrentExternalNodesDataBufferLength() {
 395         return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
 396     }
 397
 398     /**
 399      * This method returns the current phylogeny as a string in the chosen format
 400      *
 401      * @param format must be NH, NHX, NEXUS or PHYLOXML
 402      * @return the phylogeny string
 403      * @author Herve Menager
 404      */
 405     public String getCurrentPhylogeny( final String format ) {
 406         removeAllTextFrames();
 407         if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
 408                 || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
 409             return new String();
 410         }
 411         switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
 412             case NH:
 413                 return getMainPanel().getCurrentPhylogeny().toNewHampshire();
 414             case NHX:
 415                 return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
 416             case NEXUS:
 417                 return getMainPanel().getCurrentPhylogeny().toNexus();
 418             case PHYLOXML:
 419                 return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
 420             default:
 421                 break;
 422         }
 423         return new String();
 424     }
 425
 426     /**
 427      * This method returns a view of the current phylogeny in a chosen
 428      * graphics format, base64-encoded in a string so that in can be used
 429      * from javascript.
 430      *
 431      * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
 432      * @return the phylogeny string
 433      * @author Herve Menager
 434      */
 435     public String getCurrentPhylogenyGraphicsAsBase64EncodedString( final String format ) {
 436         final ByteArrayOutputStream baos = new ByteArrayOutputStream();
 437         try {
 438             AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
 439                                                                     _mainpanel.getWidth(),
 440                                                                     _mainpanel.getHeight(),
 441                                                                     getCurrentTreePanel(),
 442                                                                     getCurrentTreePanel().getControlPanel(),
 443                                                                     GraphicsExportType.valueOf( format ),
 444                                                                     getOptions() );
 445         }
 446         catch ( final IOException ioe ) {
 447             ForesterUtil.printErrorMessage( NAME, ioe.toString() );
 448             ioe.printStackTrace();
 449             JOptionPane.showMessageDialog( this,
 450                                            NAME + ": Failed to generate graphics: " + "\nException: " + ioe,
 451                                            "Failed to generate graphics",
 452                                            JOptionPane.ERROR_MESSAGE );
 453             return null;
 454         }
 455         final byte[] bytes = baos.toByteArray();
 456         final String dataImg = Base64.encodeBase64String( bytes );
 457         return dataImg;
 458     }
 459
 460     public Options getOptions() {
 461         return _options;
 462     }
 463
 464     @Override
 465     public void init() {
 466         final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
 467         AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
 468         final Configuration configuration = new Configuration( config_filename, true, true, true );
 469         setConfiguration( configuration );
 470         setOptions( Options.createInstance( configuration ) );
 471         setupUI();
 472         final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 473         if ( ForesterUtil.isEmpty( tree_url_str ) ) {
 474             ForesterUtil.printErrorMessage( NAME, "could not get tree URL from "
 475                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 476             JOptionPane.showMessageDialog( this, NAME + ": could not get tree URL from "
 477                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD, "Failed get URL", JOptionPane.ERROR_MESSAGE );
 478             return;
 479         }
 480         AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
 481         // Get URL to tree file
 482         URL phys_url = null;
 483         try {
 484             phys_url = new URL( tree_url_str );
 485         }
 486         catch ( final Exception e ) {
 487             ForesterUtil.printErrorMessage( NAME, "error: " + e );
 488             e.printStackTrace();
 489             JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
 490                     + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
 491         }
 492         if ( phys_url == null ) {
 493             ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from "
 494                     + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
 495             JOptionPane.showMessageDialog( this,
 496                                            NAME + ": Could not create URL from: \"" + tree_url_str,
 497                                            "Failed to create URL",
 498                                            JOptionPane.ERROR_MESSAGE );
 499             return;
 500         }
 501         // Load the tree from URL
 502         Phylogeny[] phys = null;
 503         try {
 504             phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
 505                                                     getConfiguration().isValidatePhyloXmlAgainstSchema(),
 506                                                     getConfiguration().isReplaceUnderscoresInNhParsing(),
 507                                                     getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
 508                                                     getConfiguration().getTaxonomyExtraction(),
 509                                                     getConfiguration().isMidpointReroot() );
 510         }
 511         catch ( final Exception e ) {
 512             ForesterUtil.printErrorMessage( NAME, e.toString() );
 513             e.printStackTrace();
 514             JOptionPane.showMessageDialog( this,
 515                                            NAME + ": Failed to read phylogenies: " + "\nException: " + e,
 516                                            "Failed to read phylogenies",
 517                                            JOptionPane.ERROR_MESSAGE );
 518         }
 519         if ( phys == null ) {
 520             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null" );
 521             JOptionPane.showMessageDialog( this,
 522                                            NAME + ": phylogenies from [" + phys_url + "] are null",
 523                                            "Failed to read phylogenies",
 524                                            JOptionPane.ERROR_MESSAGE );
 525             return;
 526         }
 527         else if ( phys.length < 1 ) {
 528             ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are empty" );
 529             JOptionPane.showMessageDialog( this,
 530                                            NAME + ": phylogenies from [" + phys_url + "] are empty",
 531                                            "Failed to read phylogenies",
 532                                            JOptionPane.ERROR_MESSAGE );
 533             return;
 534         }
 535         else {
 536             AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
 537         }
 538         //
 539         final String species_tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD );
 540         if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) {
 541             AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" );
 542             Phylogeny[] species_trees = null;
 543             try {
 544                 final URL species_tree_url = new URL( species_tree_url_str );
 545                 species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
 546                                                                  configuration.isValidatePhyloXmlAgainstSchema(),
 547                                                                  configuration.isReplaceUnderscoresInNhParsing(),
 548                                                                  false,
 549                                                                  TAXONOMY_EXTRACTION.NO,
 550                                                                  false );
 551             }
 552             catch ( final IOException e ) {
 553                 ForesterUtil.printErrorMessage( NAME, "could not read species tree from  [" + species_tree_url_str
 554                         + "]" );
 555                 JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from  ["
 556                         + species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE );
 557             }
 558             if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
 559                 AptxUtil.printAppletMessage( NAME, "successfully read species tree" );
 560                 if ( species_trees[ 0 ].isEmpty() ) {
 561                     ForesterUtil.printErrorMessage( NAME, "species tree is empty" );
 562                 }
 563                 else if ( !species_trees[ 0 ].isRooted() ) {
 564                     ForesterUtil.printErrorMessage( NAME, "species tree is not rooted" );
 565                 }
 566                 else {
 567                     setSpeciesTree( species_trees[ 0 ] );
 568                     AptxUtil.printAppletMessage( NAME, "species tree OK" );
 569                 }
 570             }
 571         }
 572         //
 573         setVisible( false );
 574         setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
 575         _jmenubar = new JMenuBar();
 576         if ( !getConfiguration().isHideControlPanelAndMenubar() ) {
 577             if ( !getConfiguration().isUseNativeUI() ) {
 578                 _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 579             }
 580             if ( getSpeciesTree() != null ) {
 581                 buildAnalysisMenu();
 582             }
 583             buildToolsMenu();
 584             buildViewMenu();
 585             buildFontSizeMenu();
 586             buildOptionsMenu();
 587             buildTypeMenu();
 588             buildHelpMenu();
 589             setJMenuBar( _jmenubar );
 590         }
 591         final Container contentpane = getContentPane();
 592         contentpane.setLayout( new BorderLayout() );
 593         contentpane.add( getMainPanel(), BorderLayout.CENTER );
 594         addComponentListener( new ComponentAdapter() {
 595
 596             @Override
 597             public void componentResized( final ComponentEvent e ) {
 598                 if ( getMainPanel().getCurrentTreePanel() != null ) {
 599                     getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel()
 600                                                                                             .getCurrentTreePanel()
 601                                                                                             .getWidth(),
 602                                                                                     getMainPanel()
 603                                                                                             .getCurrentTreePanel()
 604                                                                                             .getHeight(),
 605                                                                                     getOptions()
 606                                                                                             .isAllowFontSizeChange() );
 607                 }
 608             }
 609         } );
 610         if ( getConfiguration().isUseTabbedDisplay() ) {
 611             try {
 612                 AptxUtil.printAppletMessage( NAME, "using tabbed display" );
 613                 AptxUtil.addPhylogeniesToTabs( phys,
 614                                                new File( phys_url.getFile() ).getName(),
 615                                                phys_url.toString(),
 616                                                getConfiguration(),
 617                                                getMainPanel() );
 618             }
 619             catch ( final Exception e ) {
 620                 ForesterUtil.printErrorMessage( NAME, e.toString() );
 621                 e.printStackTrace();
 622             }
 623         }
 624         else {
 625             AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
 626             if ( getSpeciesTree() != null ) {
 627                 AptxUtil.printAppletMessage( NAME,
 628                                              "Warning: gsdi (gene duplication inference) only available tabbed display" );
 629             }
 630             AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
 631         }
 632         try {
 633             validate();
 634             setName( NAME );
 635             getMainPanel().getControlPanel().showWholeAll();
 636             getMainPanel().getControlPanel().showWhole();
 637             /* GUILHEM_BEG */
 638             getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
 639             for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
 640                     .getRelevantSequenceRelationTypes() ) {
 641                 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
 642             }
 643             final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
 644             if ( default_relation != null ) {
 645                 getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
 646             }
 647             final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
 648             if ( default_sequence != null ) {
 649                 getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
 650             }
 651             /* GUILHEM_END */
 652             System.gc();
 653             AptxUtil.printAppletMessage( NAME, "successfully initialized" );
 654             setVisible( true );
 655         }
 656         catch ( final Exception e ) {
 657             ForesterUtil.printErrorMessage( NAME, e.toString() );
 658             e.printStackTrace();
 659         }
 660     }
 661
 662     public void showTextFrame( final String s, final String title ) {
 663         checkTextFrames();
 664         _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
 665     }
 666
 667     @Override
 668     public void start() {
 669         if ( getMainPanel() != null ) {
 670             getMainPanel().validate();
 671         }
 672         requestFocus();
 673         requestFocusInWindow();
 674         requestFocus();
 675         AptxUtil.printAppletMessage( NAME, "started" );
 676     }
 677
 678     void buildAnalysisMenu() {
 679         _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
 680         _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
 681         _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
 682         customizeJMenuItem( _gsdi_item );
 683         customizeJMenuItem( _gsdir_item );
 684         //  _analysis_menu.addSeparator();
 685         //  _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
 686         //  customizeJMenuItem( _lineage_inference );
 687         //  _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
 688         _jmenubar.add( _analysis_menu );
 689     }
 690
 691     void buildFontSizeMenu() {
 692         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
 693         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
 694         _font_size_menu.add( _tiny_fonts_mi = new JMenuItem( "Tiny fonts" ) );
 695         _font_size_menu.add( _small_fonts_mi = new JMenuItem( "Small fonts" ) );
 696         _font_size_menu.add( _medium_fonts_mi = new JMenuItem( "Medium fonts" ) );
 697         _font_size_menu.add( _large_fonts_mi = new JMenuItem( "Large fonts" ) );
 698         customizeJMenuItem( _super_tiny_fonts_mi );
 699         customizeJMenuItem( _tiny_fonts_mi );
 700         customizeJMenuItem( _small_fonts_mi );
 701         customizeJMenuItem( _medium_fonts_mi );
 702         customizeJMenuItem( _large_fonts_mi );
 703         _jmenubar.add( _font_size_menu );
 704     }
 705
 706     void buildHelpMenu() {
 707         _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
 708         _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );
 709         _help_jmenu.addSeparator();
 710         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
 711         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
 712         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
 713         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
 714         _help_jmenu.addSeparator();
 715         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
 716         customizeJMenuItem( _help_item );
 717         customizeJMenuItem( _website_item );
 718         customizeJMenuItem( _phyloxml_website_item );
 719         customizeJMenuItem( _aptx_ref_item );
 720         customizeJMenuItem( _phyloxml_ref_item );
 721         customizeJMenuItem( _about_item );
 722         _phyloxml_ref_item.setToolTipText( MainFrame.PHYLOXML_REF_TOOL_TIP );
 723         _aptx_ref_item.setToolTipText( MainFrame.APTX_REF_TOOL_TIP );
 724         _jmenubar.add( _help_jmenu );
 725     }
 726
 727     void buildOptionsMenu() {
 728         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
 729         _options_jmenu.addChangeListener( new ChangeListener() {
 730
 731             @Override
 732             public void stateChanged( final ChangeEvent e ) {
 733                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
 734                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
 735                 MainFrame
 736                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
 737                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
 738                         .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
 739                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
 740                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
 741                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
 742                 try {
 743                     getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
 744                     getMainPanel().getControlPanel().setVisibilityOfX();
 745                 }
 746                 catch ( final Exception ignore ) {
 747                     // do nothing, not important.
 748                 }
 749             }
 750         } );
 751         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
 752                                                                 getConfiguration() ) );
 753         _options_jmenu
 754                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
 755         _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
 756         _options_jmenu
 757                 .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
 758         _radio_group_1 = new ButtonGroup();
 759         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
 760         _radio_group_1.add( _uniform_cladograms_rbmi );
 761         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
 762         /////
 763         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
 764         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
 765         _options_jmenu
 766                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
 767         _options_jmenu
 768                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
 769         _options_jmenu
 770                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
 771         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
 772             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
 773             _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
 774         }
 775         _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
 776         _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
 777         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
 778         _options_jmenu
 779                 .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
 780         _options_jmenu
 781                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
 782         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
 783         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
 784         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
 785         _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
 786         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
 787         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
 788         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
 789         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
 790         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
 791         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
 792         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
 793         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
 794         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
 795         /////
 796         _options_jmenu.addSeparator();
 797         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
 798                                                                 getConfiguration() ) );
 799         _options_jmenu
 800                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
 801         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
 802         _options_jmenu
 803                 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
 804         customizeJMenuItem( _choose_font_mi );
 805         customizeJMenuItem( _choose_minimal_confidence_mi );
 806         customizeJMenuItem( _switch_colors_mi );
 807         customizeJMenuItem( _overview_placment_mi );
 808         customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
 809         customizeCheckBoxMenuItem( _label_direction_cbmi,
 810                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
 811         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
 812         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
 813         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
 814         customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
 815         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
 816         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
 817                 .isShowDefaultNodeShapesExternal() );
 818         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
 819                 .isShowDefaultNodeShapesInternal() );
 820         customizeJMenuItem( _cycle_node_shape_mi );
 821         customizeJMenuItem( _cycle_node_fill_mi );
 822         customizeJMenuItem( _choose_node_size_mi );
 823         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
 824         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
 825         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
 826         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
 827                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
 828         customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
 829                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
 830         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
 831                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
 832         customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
 833         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
 834         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
 835         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
 836         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
 837         customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
 838         customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
 839         _jmenubar.add( _options_jmenu );
 840     }
 841
 842     void buildToolsMenu() {
 843         _tools_menu = MainFrame.createMenu( "Tools", getConfiguration() );
 844         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
 845         customizeJMenuItem( _confcolor_item );
 846         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
 847         customizeJMenuItem( _taxcolor_item );
 848         _tools_menu.addSeparator();
 849         _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
 850         _remove_visual_styles_item
 851                 .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
 852         customizeJMenuItem( _remove_visual_styles_item );
 853         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
 854         _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );
 855         customizeJMenuItem( _remove_branch_color_item );
 856         _tools_menu.addSeparator();
 857         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
 858         customizeJMenuItem( _midpoint_root_item );
 859         _tools_menu.addSeparator();
 860         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
 861         customizeJMenuItem( _collapse_species_specific_subtrees );
 862         _jmenubar.add( _tools_menu );
 863     }
 864
 865     void buildTypeMenu() {
 866         _type_menu = MainFrame.createMenu( MainFrame.TYPE_MENU_HEADER, getConfiguration() );
 867         _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
 868         _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
 869         _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
 870         _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
 871         _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
 872         _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
 873         _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
 874         _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
 875         customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
 876         customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
 877         customizeCheckBoxMenuItem( _euro_type_cbmi, false );
 878         customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
 879         customizeCheckBoxMenuItem( _curved_type_cbmi, false );
 880         customizeCheckBoxMenuItem( _convex_type_cbmi, false );
 881         customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
 882         customizeCheckBoxMenuItem( _circular_type_cbmi, false );
 883         _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 884         _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
 885         initializeTypeMenu( getOptions() );
 886         _jmenubar.add( _type_menu );
 887     }
 888
 889     void buildViewMenu() {
 890         _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
 891         _view_jmenu
 892                 .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
 893         _view_jmenu.addSeparator();
 894         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
 895         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
 896         _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
 897         customizeJMenuItem( _display_basic_information_item );
 898         customizeJMenuItem( _view_as_NH_item );
 899         customizeJMenuItem( _view_as_XML_item );
 900         customizeJMenuItem( _view_as_nexus_item );
 901         _jmenubar.add( _view_jmenu );
 902     }
 903
 904     void checkTextFrames() {
 905         if ( _textframes.size() > 5 ) {
 906             try {
 907                 if ( _textframes.getFirst() != null ) {
 908                     _textframes.getFirst().removeMe();
 909                 }
 910                 else {
 911                     _textframes.removeFirst();
 912                 }
 913             }
 914             catch ( final NoSuchElementException e ) {
 915                 // Ignore.
 916             }
 917         }
 918     }
 919
 920     void clearCurrentExternalNodesDataBuffer() {
 921         getCurrentTreePanel().clearCurrentExternalNodesDataBuffer();
 922     }
 923
 924     void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
 925         if ( item != null ) {
 926             item.setFont( MainFrame.menu_font );
 927             if ( !getConfiguration().isUseNativeUI() ) {
 928                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 929                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
 930             }
 931             item.setSelected( is_selected );
 932             item.addActionListener( this );
 933         }
 934     }
 935
 936     void customizeJMenuItem( final JMenuItem jmi ) {
 937         jmi.setFont( MainFrame.menu_font );
 938         if ( !getConfiguration().isUseNativeUI() ) {
 939             jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 940             jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
 941         }
 942         jmi.addActionListener( this );
 943     }
 944
 945     void displayBasicInformation() {
 946         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
 947             String title = "Basic Information";
 948             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
 949                 title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
 950             }
 951             showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny(), null ), title );
 952         }
 953     }
 954
 955     void executeGSDI() {
 956         if ( !isOKforSDI( false, true ) ) {
 957             return;
 958         }
 959         if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
 960             JOptionPane.showMessageDialog( this,
 961                                            "Gene tree is not rooted.",
 962                                            "Cannot execute GSDI",
 963                                            JOptionPane.ERROR_MESSAGE );
 964             return;
 965         }
 966         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
 967         gene_tree.setAllNodesToNotCollapse();
 968         gene_tree.recalculateNumberOfExternalDescendants( false );
 969         GSDI gsdi = null;
 970         final Phylogeny species_tree = _species_tree.copy();
 971         try {
 972             gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
 973         }
 974         catch ( final SDIException e ) {
 975             JOptionPane.showMessageDialog( this,
 976                                            e.getLocalizedMessage(),
 977                                            "Error during GSDI",
 978                                            JOptionPane.ERROR_MESSAGE );
 979             return;
 980         }
 981         catch ( final Exception e ) {
 982             AptxUtil.unexpectedException( e );
 983             return;
 984         }
 985         gene_tree.setRerootable( false );
 986         gene_tree.clearHashIdToNodeMap();
 987         gene_tree.recalculateNumberOfExternalDescendants( true );
 988         _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
 989         getMainPanel().getControlPanel().setShowEvents( true );
 990         showWhole();
 991         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
 992         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
 993         showWhole();
 994         _mainpanel.getTabbedPane().setSelectedIndex( selected );
 995         showWhole();
 996         _mainpanel.getCurrentTreePanel().setEdited( true );
 997         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
 998         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
 999             JOptionPane.showMessageDialog( this,
1000                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1001                                                    + "Potential duplications: "
1002                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
1003                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
1004                                                    + "Stripped gene tree nodes: "
1005                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
1006                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
1007                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1008                                            "GSDI successfully completed",
1009                                            JOptionPane.WARNING_MESSAGE );
1010         }
1011         else {
1012             JOptionPane.showMessageDialog( this,
1013                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
1014                                                    + "Potential duplications: "
1015                                                    + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
1016                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
1017                                                    + "Stripped gene tree nodes: "
1018                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
1019                                                    + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
1020                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1021                                            "GSDI successfully completed",
1022                                            JOptionPane.INFORMATION_MESSAGE );
1023         }
1024     }
1025
1026     void executeGSDIR() {
1027         if ( !isOKforSDI( false, false ) ) {
1028             return;
1029         }
1030         final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
1031         if ( ( p > 0 )
1032                 && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
1033             JOptionPane.showMessageDialog( this,
1034                                            "Gene tree is not completely binary",
1035                                            "Cannot execute GSDI",
1036                                            JOptionPane.ERROR_MESSAGE );
1037             return;
1038         }
1039         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
1040         gene_tree.setAllNodesToNotCollapse();
1041         gene_tree.recalculateNumberOfExternalDescendants( false );
1042         GSDIR gsdir = null;
1043         final Phylogeny species_tree = _species_tree.copy();
1044         try {
1045             gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
1046         }
1047         catch ( final SDIException e ) {
1048             JOptionPane.showMessageDialog( this,
1049                                            e.getLocalizedMessage(),
1050                                            "Error during GSDIR",
1051                                            JOptionPane.ERROR_MESSAGE );
1052             return;
1053         }
1054         catch ( final Exception e ) {
1055             AptxUtil.unexpectedException( e );
1056             return;
1057         }
1058         final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
1059         result_gene_tree.setRerootable( false );
1060         result_gene_tree.clearHashIdToNodeMap();
1061         result_gene_tree.recalculateNumberOfExternalDescendants( true );
1062         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
1063         _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
1064         getMainPanel().getControlPanel().setShowEvents( true );
1065         showWhole();
1066         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
1067         _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
1068         showWhole();
1069         _mainpanel.getTabbedPane().setSelectedIndex( selected );
1070         showWhole();
1071         _mainpanel.getCurrentTreePanel().setEdited( true );
1072         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
1073         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
1074             JOptionPane.showMessageDialog( this,
1075                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1076                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1077                                                    + "Stripped gene tree nodes: "
1078                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1079                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1080                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1081                                            "GSDIR successfully completed",
1082                                            JOptionPane.WARNING_MESSAGE );
1083         }
1084         else {
1085             JOptionPane.showMessageDialog( this,
1086                                            "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
1087                                                    + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
1088                                                    + "Stripped gene tree nodes: "
1089                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
1090                                                    + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
1091                                                    + "Number of polytomies in species tree used: " + poly + "\n",
1092                                            "GSDIR successfully completed",
1093                                            JOptionPane.INFORMATION_MESSAGE );
1094         }
1095     }
1096
1097     Configuration getConfiguration() {
1098         return _configuration;
1099     }
1100
1101     TreePanel getCurrentTreePanel() {
1102         return getMainPanel().getCurrentTreePanel();
1103     }
1104
1105     JCheckBoxMenuItem getlabelDirectionCbmi() {
1106         return _label_direction_cbmi;
1107     }
1108
1109     Options getOtions() {
1110         return _options;
1111     }
1112
1113     void initializeTypeMenu( final Options options ) {
1114         setTypeMenuToAllUnselected();
1115         try {
1116             switch ( options.getPhylogenyGraphicsType() ) {
1117                 case CONVEX:
1118                     _convex_type_cbmi.setSelected( true );
1119                     break;
1120                 case CURVED:
1121                     _curved_type_cbmi.setSelected( true );
1122                     break;
1123                 case EURO_STYLE:
1124                     _euro_type_cbmi.setSelected( true );
1125                     break;
1126                 case ROUNDED:
1127                     _rounded_type_cbmi.setSelected( true );
1128                     break;
1129                 case TRIANGULAR:
1130                     _triangular_type_cbmi.setSelected( true );
1131                     break;
1132                 case UNROOTED:
1133                     _unrooted_type_cbmi.setSelected( true );
1134                     break;
1135                 case CIRCULAR:
1136                     _circular_type_cbmi.setSelected( true );
1137                     break;
1138                 default:
1139                     _rectangular_type_cbmi.setSelected( true );
1140                     break;
1141             }
1142         }
1143         catch ( final NullPointerException np ) {
1144             // In all likelihood, this is caused by menu-less display.
1145         }
1146     }
1147
1148     boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
1149         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1150             return false;
1151         }
1152         else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
1153             JOptionPane.showMessageDialog( this,
1154                                            "No species tree loaded",
1155                                            "Cannot execute GSDI",
1156                                            JOptionPane.ERROR_MESSAGE );
1157             return false;
1158         }
1159         else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
1160             JOptionPane.showMessageDialog( this,
1161                                            "Species tree is not completely binary",
1162                                            "Cannot execute GSDI",
1163                                            JOptionPane.ERROR_MESSAGE );
1164             return false;
1165         }
1166         else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
1167             JOptionPane.showMessageDialog( this,
1168                                            "Gene tree is not completely binary",
1169                                            "Cannot execute GSDI",
1170                                            JOptionPane.ERROR_MESSAGE );
1171             return false;
1172         }
1173         else {
1174             return true;
1175         }
1176     }
1177
1178     boolean isSubtreeDisplayed() {
1179         if ( getCurrentTreePanel() != null ) {
1180             if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
1181                 JOptionPane
1182                         .showMessageDialog( this,
1183                                             "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
1184                                             "Operation can not be exectuted on a sub-tree",
1185                                             JOptionPane.WARNING_MESSAGE );
1186                 return true;
1187             }
1188         }
1189         return false;
1190     }
1191
1192     void removeAllTextFrames() {
1193         for( final TextFrame tf : _textframes ) {
1194             if ( tf != null ) {
1195                 tf.close();
1196             }
1197         }
1198         _textframes.clear();
1199     }
1200
1201     void setConfiguration( final Configuration configuration ) {
1202         _configuration = configuration;
1203     }
1204
1205     void setOptions( final Options options ) {
1206         _options = options;
1207     }
1208
1209     void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
1210         setTypeMenuToAllUnselected();
1211         try {
1212             switch ( type ) {
1213                 case CIRCULAR:
1214                     _circular_type_cbmi.setSelected( true );
1215                     break;
1216                 case CONVEX:
1217                     _convex_type_cbmi.setSelected( true );
1218                     break;
1219                 case CURVED:
1220                     _curved_type_cbmi.setSelected( true );
1221                     break;
1222                 case EURO_STYLE:
1223                     _euro_type_cbmi.setSelected( true );
1224                     break;
1225                 case ROUNDED:
1226                     _rounded_type_cbmi.setSelected( true );
1227                     break;
1228                 case RECTANGULAR:
1229                     _rectangular_type_cbmi.setSelected( true );
1230                     break;
1231                 case TRIANGULAR:
1232                     _triangular_type_cbmi.setSelected( true );
1233                     break;
1234                 case UNROOTED:
1235                     _unrooted_type_cbmi.setSelected( true );
1236                     break;
1237                 default:
1238                     throw new IllegalArgumentException( "unknown type: " + type );
1239             }
1240         }
1241         catch ( final NullPointerException np ) {
1242             // In all likelihood, this is caused by menu-less display.
1243         }
1244     }
1245
1246     void setTypeMenuToAllUnselected() {
1247         if ( _convex_type_cbmi != null ) {
1248             _convex_type_cbmi.setSelected( false );
1249         }
1250         if ( _curved_type_cbmi != null ) {
1251             _curved_type_cbmi.setSelected( false );
1252         }
1253         if ( _euro_type_cbmi != null ) {
1254             _euro_type_cbmi.setSelected( false );
1255         }
1256         if ( _rounded_type_cbmi != null ) {
1257             _rounded_type_cbmi.setSelected( false );
1258         }
1259         if ( _triangular_type_cbmi != null ) {
1260             _triangular_type_cbmi.setSelected( false );
1261         }
1262         if ( _rectangular_type_cbmi != null ) {
1263             _rectangular_type_cbmi.setSelected( false );
1264         }
1265         if ( _unrooted_type_cbmi != null ) {
1266             _unrooted_type_cbmi.setSelected( false );
1267         }
1268         if ( _circular_type_cbmi != null ) {
1269             _circular_type_cbmi.setSelected( false );
1270         }
1271     }
1272
1273     void showWhole() {
1274         _mainpanel.getControlPanel().showWhole();
1275     }
1276
1277     void switchColors() {
1278         final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
1279         final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
1280         csc.setVisible( true );
1281         getMainPanel().setTreeColorSet( colorset );
1282     }
1283
1284     void typeChanged( final Object o ) {
1285         updateTypeCheckboxes( getOptions(), o );
1286         updateOptions( getOptions() );
1287         if ( getCurrentTreePanel() != null ) {
1288             final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
1289             final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
1290             if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1291                     || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
1292                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
1293                     || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
1294                 getCurrentTreePanel().getControlPanel().showWhole();
1295             }
1296             if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1297                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
1298             }
1299             else {
1300                 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
1301             }
1302             getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
1303             MainFrame.updateScreenTextAntialias( getMainPanel().getTreePanels() );
1304         }
1305     }
1306
1307     void updateOptions( final Options options ) {
1308         options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
1309         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
1310                 && _background_gradient_cbmi.isSelected() );
1311         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
1312         options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
1313                 && _show_annotation_ref_source.isSelected() );
1314         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
1315                 && _abbreviate_scientific_names.isSelected() );
1316         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
1317                 && _color_labels_same_as_parent_branch.isSelected() );
1318         options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
1319                 && _show_default_node_shapes_internal_cbmi.isSelected() );
1320         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
1321                 && _show_default_node_shapes_external_cbmi.isSelected() );
1322         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
1323             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
1324         }
1325         else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
1326             options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
1327         }
1328         else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
1329             options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
1330         }
1331         options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
1332                 && _search_case_senstive_cbmi.isSelected() );
1333         if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
1334             options.setShowScale( _show_scale_cbmi.isSelected() );
1335         }
1336         if ( _label_direction_cbmi != null ) {
1337             if ( _label_direction_cbmi.isSelected() ) {
1338                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1339             }
1340             else {
1341                 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1342             }
1343         }
1344         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
1345         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
1346                 && _show_confidence_stddev_cbmi.isSelected() );
1347         if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
1348             options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
1349         }
1350         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
1351                 && _search_whole_words_only_cbmi.isSelected() );
1352         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
1353                 && _inverse_search_result_cbmi.isSelected() );
1354         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
1355             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1356         }
1357         else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
1358             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
1359         }
1360         else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
1361             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
1362         }
1363         else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
1364             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
1365         }
1366         else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
1367             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
1368         }
1369         else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
1370             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
1371         }
1372         else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
1373             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1374         }
1375         else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
1376             options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
1377         }
1378         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
1379             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
1380         }
1381         if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
1382             options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
1383         }
1384         if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
1385             options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
1386         }
1387     }
1388
1389     void updateTypeCheckboxes( final Options options, final Object o ) {
1390         setTypeMenuToAllUnselected();
1391         ( ( JCheckBoxMenuItem ) o ).setSelected( true );
1392     }
1393
1394     void viewAsNexus() {
1395         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1396             String title = "Nexus";
1397             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1398                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1399             }
1400             showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
1401                                    .getNhConversionSupportValueStyle() ),
1402                            title );
1403         }
1404     }
1405
1406     void viewAsNH() {
1407         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1408             String title = "New Hampshire";
1409             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1410                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1411             }
1412             showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire( getOptions()
1413                                    .getNhConversionSupportValueStyle() ),
1414                            title );
1415         }
1416     }
1417
1418     void viewAsXML() {
1419         if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) {
1420             String title = "phyloXML";
1421             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
1422                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
1423             }
1424             showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title );
1425         }
1426     }
1427
1428     private void chooseFont() {
1429         final FontChooser fc = new FontChooser();
1430         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
1431         fc.showDialog( this, "Select the Base Font" );
1432         getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
1433     }
1434
1435     private void chooseMinimalConfidence() {
1436         final String s = ( String ) JOptionPane
1437                 .showInputDialog( this,
1438                                   "Please the minimum for confidence values to be displayed.\n" + "[current value: "
1439                                           + getOptions().getMinConfidenceValue() + "]\n",
1440                                   "Minimal Confidence Value",
1441                                   JOptionPane.QUESTION_MESSAGE,
1442                                   null,
1443                                   null,
1444                                   getOptions().getMinConfidenceValue() );
1445         if ( !ForesterUtil.isEmpty( s ) ) {
1446             boolean success = true;
1447             double m = 0.0;
1448             final String m_str = s.trim();
1449             if ( !ForesterUtil.isEmpty( m_str ) ) {
1450                 try {
1451                     m = Double.parseDouble( m_str );
1452                 }
1453                 catch ( final Exception ex ) {
1454                     success = false;
1455                 }
1456             }
1457             else {
1458                 success = false;
1459             }
1460             if ( success && ( m >= 0.0 ) ) {
1461                 getOptions().setMinConfidenceValue( m );
1462             }
1463         }
1464     }
1465
1466     private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
1467         if ( item != null ) {
1468             item.setFont( MainFrame.menu_font );
1469             if ( !getConfiguration().isUseNativeUI() ) {
1470                 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
1471                 item.setForeground( getConfiguration().getGuiMenuTextColor() );
1472             }
1473             item.setSelected( is_selected );
1474             item.addActionListener( this );
1475         }
1476     }
1477
1478     private MainPanel getMainPanel() {
1479         return _mainpanel;
1480     }
1481
1482     private Phylogeny getSpeciesTree() {
1483         return _species_tree;
1484     }
1485
1486     private boolean isScreenAntialias() {
1487         return true;
1488     }
1489
1490     private void removeBranchColors() {
1491         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1492             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
1493         }
1494     }
1495
1496     private void removeVisualStyles() {
1497         if ( getMainPanel().getCurrentPhylogeny() != null ) {
1498             AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
1499         }
1500     }
1501
1502     private void setMainPanel( final MainPanelApplets main_panel ) {
1503         _mainpanel = main_panel;
1504     }
1505
1506     private void setSpeciesTree( final Phylogeny species_tree ) {
1507         _species_tree = species_tree;
1508     }
1509
1510     private void setupUI() {
1511         try {
1512             if ( getConfiguration().isUseNativeUI() ) {
1513                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
1514             }
1515             else {
1516                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
1517             }
1518         }
1519         catch ( final UnsupportedLookAndFeelException e ) {
1520             AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
1521         }
1522         catch ( final ClassNotFoundException e ) {
1523             AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
1524         }
1525         catch ( final InstantiationException e ) {
1526             AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
1527         }
1528         catch ( final IllegalAccessException e ) {
1529             AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
1530         }
1531         catch ( final Exception e ) {
1532             AptxUtil.dieWithSystemError( e.toString() );
1533         }
1534     }
1535
1536     static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
1537         for( final TreePanel tree_panel : treepanels ) {
1538             tree_panel.setTextAntialias();
1539         }
1540     }
1541 }